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    Kang Jin

    Kang.Jin at cchmc.org [Github] [Google Scholar] [Twitter]
    Last updated: 02/25/2023

    Research Interest

    Hi, I am a fifth-year Ph.D. student in Biomedical Informatics Division under the supervision of Dr. Bruce Aronow at Cincinnati Children’s Hospital.

    As an enthusiastic researcher, my passion lies in leveraging advanced computational methods to unravel high-throughput sequencing data for single cell profiling. My current research endeavors are primarily centered around developing deep learning and probabilistic models to analyze spatial subcellular omics data (Jin et al., MLCB2022, wrapping up) and temporal perturbation patterns in single-cell experiments (Jin et al., Briefings in Bioinformatics, 2022). I have also contributed to the field by creating an interactive platform called ToppCell for large-scale single cell data exploration (Jin et al. iScience, 2021), which enables the investigation of perturbation effects of single cell data in various biological systems and diseases, including HLHS (Xu et al., Cell Stem Cell, 2022), schizophrenia (Sebastian*, Jin* et al. Nat Communications, In Revision), hepatoplastoma (Bondoc*, Glaser*, Jin* et al. Communications Biology, 2021), lung fibrosis (Sun et al. Developmental Cell, 2022) and COVID-19.

    I am particularly interested in cutting-edge bioengineering innovations, such as single-cell multiomics profiling, spatial transcriptomics, pooled CRISPR screens and live-cell imaging. Collaborating with Dr. Jian Shu, I am currently in designing experiments and devising innovative computational approaches to understand cell states and microenvironment perturbations in subcellular resolution using image-based spatial omics technologies.

    With expertise in computational biology and a strong interest in bioengineering, my ultimate goal is to advance our understanding of complex cellular states and their changes by implementing cutting-edge computational methods with emerging single-cell and spatial genomics data.

    Position & Education

    2018 - Present, Department of Biomedical Informatics, Cincinnati Children's Hospital, University of Cincinnati,

    Ph.D. student

    2014 - 2018, Department of Life Sciences, Zhejiang University,

    Bachelor of Biological Science

    Publications

    (*Equal contribution)
    Manuscript under review

    • Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia [paper]
      Rebecca Sebastian*, Kang Jin*, Narciso Pavon, Ruby Bansal, Andrew Potter, Yoonjae Song, Juliana Babu, Rafael Gabriel, Yubing Sun, Bruce Aronow, ChangHui Pak
      bioRxiv (Nature Communications, In Revision, 2022).

    • Guided construction of single cell reference for human and mouse lung [paper]
      Minzhe Guo, Michael P Morley, Yixin Wu, Yina Du, Shuyang Zhao, Andrew Wagner, Michal Kouril, Kang Jin, ..., Yan Xu
      bioRxiv (2022).

    • KAT5 activity regulates G0-like states in human gliomas [paper]
      Anca B. Mihalas, Sonali Arora, Samantha A. O’Connor, Heather M. Feldman, John Bassett, Kelly Mitchell, Kang Jin, ..., Patrick J. Paddisons
      bioRxiv (2022).

    • Functional immune deficiency syndrome via intestinal infection in COVID-19 [paper]
      Erica T. Prates, Michael R. Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Christiane Alvarez, David Kainer, Omar Demerdash, B Kirtley Amos, Armin Geiger, John Pestian, Kang Jin, Alexis Mitelpunkt, Eric Bardes, Bruce Aronow, Daniel Jacobson
      bioRxiv (2020).

    Published papers (as main author)

    • CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data [paper] [code]
      Kang Jin, Dan Schnell, Guangyuan Li, Nathan Salomonis, Surya Prasath, Rhonda Szczesniak, Bruce J Aronow
      Briefings in Bioinformatics (2022).

    • An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses [paper] [code]
      Kang Jin, Eric E. Bardes, Alexis Mitelpunkt, Jake Y. Wang, Surbhi Bhatnagar, Soma Sengupta, Daniel Pomeranz Krummel, Marc E. Rothenberg, Bruce J. Aronow
      iScience (2021).

    • Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease [paper]
      Xinxiu Xu, Kang Jin, Abha S Bais, Wenjuan Zhu, Hisato Yagi, Timothy N Feinstein, Phong K Nguyen, Joseph D Criscione, Xiaoqin Liu, Gisela Beutner, Kalyani B Karunakaran, Krithika S Rao, Haoting He, Phillip Adams, Catherine K Kuo, Dennis Kostka, Gloria S Pryhuber, Sruti Shiva, Madhavi K Ganapathiraju, George A Porter Jr, Jiuann-Huey Ivy Lin, Bruce Aronow, Cecilia W Lo
      Cell Stem Cell (2022).

    • Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma [paper] [code]
      Alexander Bondoc*, Kathryn Glaser*, Kang Jin*, Charissa Lake, Stefano Cairo, James Geller, Gregory Tiao, Bruce Aronow
      Communications Biology (2021).

    Published papers (as contributing author)

    • LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung [paper]
      Nathan Gaddis, Joshua Fortriede, Minzhe Guo, ..., Kang Jin, ..., Nathan Salomonis, NHLBI LungMAP Consortium
      American Journal of Respiratory Cell and Molecular Biology (2022).

    • Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons [paper]
      Danny McSweeney, Rafael Gabriel, Kang Jin, Zhiping P Pang, Bruce J Aronow, ChangHui Pak
      iScience (2022).

    • A census of the lung: CellCards from LungMAP [paper]
      Xin Sun, Anne-Karina Perl, Rongbo Li, ..., Kang Jin, ..., Edward E Morrisey, NHLBI LungMAP Consortium
      Developmental Cell (2022).

    • Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons [paper]
      ChangHui Pak, Tamas Danko, Vincent R. Mirabella, Jinzhao Wang, Yingfei Liu, Madhuri Vangipuram, Sarah Grieder, Xianglong Zhang, Thomas Ward, Yu-Wen Alvin Huang, Kang Jin, ..., Thomas C. Südhof
      PNAS (2021).

    • Predicted Arabidopsis interactome resource and gene set linkage analysis: a transcriptomic analysis resource [paper]
      Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
      Plant Physiology (2018).

    Softwares

    • ToppCell: Single-cell gene module exploratory platform

    • CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data.

    • Bering: Gene colocalization-aware segmentation of image-based spatial transcriptomics using deep learning models (Wrapping up)

    Resources

    Honors and Awards

    • Second Place, Best Poster Award, ISMB 2022 (SysMod Meeting) 2022
    • Second Place in Graduate Student Research Forum (GSRF), University of Cincinnati, 2020
    • Best Application Award of Zhejiang Bioinformatics Competition,2017
    • China National Award, 2017
    • First Prize Scholarship for Excellent Students, Zhejiang University, 2017
    • Tang Lixin Scholarship for Excellent Model Student, 2017
    • Zhejiang Provincial Government Scholarship, 2016
    • Second Prize, Physics Innovation Competition in Zhejiang Province, 2015